Bugfixes for zeissimport and dataset with transformations

dataset.py

@@ -216,7 +216,7 @@ class DataSet(object):
                 Ngrid = len(self.grid)
                 
                 width, height, rotationvalue = self.imagedim_df
-                p0, p1 = self.maxdim[:2], self.maxdim[2:]
+                p0, p1 = self.lastpos[:2], self.maxdim[2:]
                 for i in range(Ngrid):
                     print(f"Processing image {i+1} of {Ngrid}")
                     names = []
@@ -271,7 +271,7 @@ class DataSet(object):
             print('error in getZval:', self.zvalimg.shape, i, j)
             j = self.zvalimg.shape[1]-1
         zp = self.zvalimg[i,j]
-        z0, z1 = self.zpositions.min(), self.zpositions.max()
+        z0, z1 = self.zpositions[0], self.zpositions[-1]
         return zp/255.*(z1-z0) + z0
         
     def mapHeight(self, x, y):
@@ -296,7 +296,7 @@ class DataSet(object):
             
         elif mode == 'bf':
             p0[0] -= self.signx*self.imagedim_bf[0]/2
-            p0[1] += self.signy*self.imagedim_bf[1]/2
+            p0[1] -= self.signy*self.imagedim_bf[1]/2
             x, y = self.signx*(p[0] - p0[0])/self.pixelscale_bf, self.signy*(p[1] - p0[1])/self.pixelscale_bf
             
         else:

zeissimporter.py

@@ -164,7 +164,10 @@ class ZeissImporter(QtWidgets.QDialog):
         z0, zn = self.zrange.z0, self.zrange.zn
         if zn<z0: 
             zn, z0 = z0, zn
-        dataset.zpositions = np.linspace(z0, zn, N)-zpc[2]
+        # zeiss z axis has large values at the surface and smaller for large particles
+        # that is why we need to invert the zpositions: zimg black corresponds to zn
+        # zimg white corresponds to z0
+        dataset.zpositions = np.linspace(z0, zn, N)[::-1]-zpc[2]
         dataset.heightmap = np.zeros(3)
         dataset.signy = 1.
         zimg = cv2imread_fix(self.zmapimgname, cv2.IMREAD_GRAYSCALE)
@@ -174,24 +177,28 @@ class ZeissImporter(QtWidgets.QDialog):
 
         pshift = self.ramanctrl.getRamanPositionShift()
         dataset.pshift = pshift
-        pixelscale = self.region.width/zimg.shape[1]
+        pixelscale = self.region.scalex*1.e6
         
         # use input image as single image aquired in one shot
-        dataset.imagedim_df = (self.region.width, self.region.height, 0.0)
+        dataset.imagedim_df = (zimg.shape[1]*pixelscale, 
+                               zimg.shape[0]*pixelscale, 0.0)
         dataset.pixelscale_df = pixelscale
         
-        dataset.imagedim_bf = (self.region.width, self.region.height, 0.0)
+        dataset.imagedim_bf = (zimg.shape[1]*pixelscale, 
+                               zimg.shape[0]*pixelscale, 0.0)
         dataset.pixelscale_bf = pixelscale
+        print('scale:', pixelscale)
+        print('dim df:', dataset.imagedim_df)
+        print('dim bf:', dataset.imagedim_bf)
         
         dataset.coordinatetransform = T, pc
         
-        # set image center as reference point in data set (use Zeiss coordinates)
+        # set image center as reference point (assume just one tile) 
+        # in data set (use Zeiss coordinates)
         p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
-        p0 = p0center-.5*np.array((self.region.width, self.region.height))
-        p1 = p0center+.5*np.array((self.region.width, self.region.height))
         dataset.readin = False
-        dataset.lastpos = p0
-        dataset.maxdim = p0 + p1
+        dataset.lastpos = p0center
+        dataset.maxdim = p0center
         
         zmin, zmax = dataset.zpositions.min(), dataset.zpositions.max()
         blur = (blur)*(255.)

zeissxml.py

@@ -39,13 +39,15 @@ class Region:
     def __init__(self):
         self.centerx, self.centery = None, None
         self.width, self.height = None, None
+        self.scalex, self.scaley = None, None
         
     def __repr__(self):
         return str(self)
     
     def __str__(self):
         return f'Region center: {self.centerx, self.centery} µm\n' + \
-               f'Region size: {self.width, self.height} µm'
+               f'Region size: {self.width, self.height} µm\n' + \
+               f'Scale: {self.scalex, self.scaley} µm/pixel' 
                
 class ZRange:
     def __init__(self):
@@ -65,6 +67,7 @@ class ZeissHandler(handler.ContentHandler):
         self.zrange = ZRange()
         self.intag = False
         self.subtag = ''
+        self.scaledim = ''
         
     def characters(self, content):
         if self.intag:
@@ -75,20 +78,27 @@ class ZeissHandler(handler.ContentHandler):
             self.markers.append(Marker(attrs['Id'], attrs['StageXPosition'],
                                        attrs['StageYPosition'], 
                                        attrs['FocusPosition']))
-        elif name == 'TileRegion' or name == 'ZStackSetup':
+        elif name == 'TileRegion' or name == 'ZStackSetup' or name == 'Scaling':
             self.intag = True
         if self.intag:
             self.content = ''
-            if name in ['First','Last','Interval']:
+            if self.subtag == 'Items' and name == 'Distance':
+                self.scaledim = attrs['Id']
+            if name in ['First','Last','Interval','Items']:
                 self.subtag = name
             
     def endElement(self, name):
-        if name == 'TileRegion' or name == 'ZStackSetup':
+        if name == 'TileRegion' or name == 'ZStackSetup' or name == 'Scaling':
             self.intag = False
         if self.intag and name == 'CenterPosition':
             self.region.centerx, self.region.centery = map(float, self.content.split(','))
         elif self.intag and name == 'ContourSize':
             self.region.width, self.region.height = map(float, self.content.split(','))
+        elif self.intag and self.subtag == 'Items' and name == 'Value':
+            if self.scaledim == 'X':
+                self.region.scalex = float(self.content)
+            elif self.scaledim == 'Y':
+                self.region.scaley = float(self.content)
         elif self.intag and name == 'Value' and \
             self.subtag in ['First','Last','Interval']:
             attrmap = {'First':'z0','Last':'zn','Interval':'dz'}